It's not the calories so much as the taste of toothpaste that can be a problem. Stimulating the taste buds creates saliva which begins the digestion process and can also be a signal to the brain to divert energy to the digestion system. That can certainly take energy away from detox for no good reason. It's best to just brush with water or some use bicarb which probably wouldn't stimulate the tastebuds.
Do you drink the water because you're thirsty? There's no need to drink a set amount of water just because you're used to it or for any other reason apart from your own thirst needs. That's one thing you can control that may be effecting the pain, if not it is something going on inside you that you may just have to wait out. It won't last forever, it is some detox or repair going on and you will be better off for it once it's done.